1887

Abstract

A novel Gram-staining-positive, rod-shaped bacterium, designated DCY100, was isolated from rhizome of mountain ginseng root in Hwacheon mountain, Gangwon province, Republic of Korea. The 16S rRNA gene sequence analysis showed that strain DCY100 belonged to the genus and was most closely related to KCTC 19189 (97.9 %), JCM 15575 (97.2 %) and DSM 19600 (97.1 %). The major menaquinones were MK-11 and MK-12. The major polar lipids were found to be diphosphatidylglycerol, phosphatidylglycerol and one unidentified glycolipid. The major fatty acids (>10.0 %) were anteiso-C, anteiso-C and iso-C. The cell-wall peptidoglycan contained the amino acids ornithine, alanine, glutamic acid and glycine; whole-cell sugars consisted of glucose, galactose, rhamnose and ribose. The DNA G+C content was 63.6 ± 0.7 mol%. The DNA–DNA hybridization relatedness values between strain DCY100 and KCTC 19189, JCM 15575 and DSM 19600 were 36.2 ± 0.4, 22.0 ± 3.0 and 15.3 ± 1.8 %, respectively. On the basis of phenotypic, chemotaxonomic and genotypic analyses, the isolate is classified as a representative of a novel species in the genus , for which the name DCY100 is proposed. The type strain is DCY100 ( = KCTC 39529 = JCM 30598).

Funding
This study was supported by the:
  • Institute of Planning and Evaluation for Technology in Food, Agriculture, Forestry and Fisheries (Award 313038-03-1-S13020)
  • Rural Development Administration, Republic of Korea (Award PJ01116602)
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2015-09-01
2024-03-29
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References

  1. Alves A., Correia A., Igual J.M., Trujillo M.E. ( 2014;). Microbacterium endophyticum sp. nov. and Microbacterium halimionae sp. nov., endophytes isolated from the salt-marsh plant Halimione portulacoides and emended description of the genus Microbacterium . Syst Appl Microbiol 37 474479 [View Article] [PubMed].
    [Google Scholar]
  2. Anzai Y., Kim H., Park J.Y., Wakabayashi H., Oyaizu H. ( 2000;). Phylogenetic affiliation of the pseudomonads based on 16S rRNA sequence. Int J Syst Evol Microbiol 50 15631589 [View Article] [PubMed].
    [Google Scholar]
  3. Bauer A.W., Kirby W.M.M., Sherris J.C., Turck M. ( 1966;). Antibiotic susceptibility testing by a standardized single disk method. Am J Clin Pathol 45 493496.
    [Google Scholar]
  4. Becker B., Lechevalier M.P., Lechevalier H.A. ( 1965;). Chemical composition of cell-wall preparations from strains of various form-genera of aerobic actinomycetes. Appl Microbiol 13 236243.
    [Google Scholar]
  5. Bernardet J.F., Nakagawa Y., Holmes B. Subcommittee on the taxonomy of Flavobacterium and Cytophaga-like bacteria of the International Committee on Systematics of Prokaryotes ( 2002;). Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 52 10491070 [View Article] [PubMed].
    [Google Scholar]
  6. Christensen W.B. ( 1946;). Urea decomposition as a means of differentiating Proteus and paracolon cultures from each other and from Salmonella and Shigella types. J Bacteriol 52 461466.
    [Google Scholar]
  7. Collins M.D., Jones D. ( 1981;). Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. Microbiol Rev 45 316354.
    [Google Scholar]
  8. Collins M.D., Jones D., Kroppenstedt R.M. ( 1983;). Reclassification of Brevibacterium imperiale (Steinhaus) and Corynebacterium laevaniformans (Dias and Bhat) in a Redefined Genus Microbacterium (Orla-Jensen), as Microbacterium imperiale comb. nov. and Microbacterium laevaniformans nom. rev.; comb. nov. Syst Appl Microbiol 4 6578 [View Article] [PubMed].
    [Google Scholar]
  9. Ezaki T., Hashimoto Y., Yabuuchi E. ( 1989;). Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Bacteriol 39 224229 [View Article].
    [Google Scholar]
  10. Felsenstein J. ( 1985;). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39 783791 [View Article].
    [Google Scholar]
  11. Fitch W.M. ( 1971;). Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20 406416 [View Article].
    [Google Scholar]
  12. Hong S.K. ( 1978;). Gingeng cultivation. . In Korean Ginseng , 2nd edn.., pp. 245278. Edited by Bae H. W. Korea: Korea Ginseng Research Institute;.
    [Google Scholar]
  13. Kageyama A., Takahashi Y., Matsuo Y., Adachi K., Kasai H., Shizuri Y., Omura S. ( 2007;). Microbacterium flavum sp. nov. and Microbacterium lacus sp. nov., isolated from marine environments. Actinomycetologica 21 5358 [View Article].
    [Google Scholar]
  14. Kim M.K., Im W.T., Ohta H., Lee M., Lee S.T. ( 2005;). Sphingopyxis granuli sp. nov., a β-glucosidase-producing bacterium in the family Sphingomonadaceae in α-4 subclass of the Proteobacteria . J Microbiol 43 152157.
    [Google Scholar]
  15. Kim O.S., Cho Y.J., Lee K., Yoon S.H., Kim M., Na H., Park S.C., Jeon Y.S., Lee J.H., other authors. ( 2012;). Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62 716721 [View Article] [PubMed].
    [Google Scholar]
  16. Kim C., Choo G.C., Cho H.S., Lim J.T. ( 2015;). Soil properties of cultivation sites for mountain-cultivated ginseng at local level. J Ginseng Res 39 7680 [View Article] [PubMed].
    [Google Scholar]
  17. Lane D.J. ( 1991;). 16S/23S rRNA sequencing. . In Nucleic Acid Techniques in Bacterial Systematics, pp. 115176. Edited by Stackebrandt E., Goodfellow M. Chichester: Wiley;.
    [Google Scholar]
  18. Lee H.J., Cho G.Y., Chung S.H., Whang K.S. ( 2014;). Streptomyces panaciradicis sp. nov., a β-glucosidase-producing bacterium isolated from ginseng rhizoplane. Int J Syst Evol Microbiol 64 38163820 [View Article] [PubMed].
    [Google Scholar]
  19. McPherson D.C., Popham D.L. ( 2003;). Peptidoglycan synthesis in the absence of class A penicillin-binding proteins in Bacillus subtilis . J Bacteriol 185 14231431 [View Article] [PubMed].
    [Google Scholar]
  20. Mesbah M., Premachandran U., Whitman W.B. ( 1989;). Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 39 159167 [View Article].
    [Google Scholar]
  21. Minnikin D.E., O' Donnell A.G., Goodfellow M., Alderson G., Athalye M., Schaal A., Parlett J.H. ( 1984;). An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2 233241 [View Article].
    [Google Scholar]
  22. Nguyen N.L., Kim Y.J., Hoang V.A., Yang D.C. ( 2013;). Chryseobacterium ginsengisoli sp. nov., isolated from the rhizosphere of ginseng and emended description of Chryseobacterium gleum . Int J Syst Evol Microbiol 63 29752980 [View Article] [PubMed].
    [Google Scholar]
  23. Orla-Jensen S. ( 1919). The Lactic Acid Bacteria., Copenhagen: Høst and Sons;.
    [Google Scholar]
  24. Park M.J., Kim M.K., Kim H.B., Im W.T., Yi T.H., Kim S.Y., Soung N.K., Yang D.C. ( 2008;). Microbacterium ginsengisoli sp. nov., a β-glucosidase-producing bacterium isolated from soil of a ginseng field. Int J Syst Evol Microbiol 58 429433 [View Article] [PubMed].
    [Google Scholar]
  25. Prescott L.M., Harley J.P. ( 2001). Laboratory Exercises in Microbiology , 5th edn.., New York: McGraw–Hill;.
    [Google Scholar]
  26. Saitou N., Nei M. ( 1987;). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4 406425.
    [Google Scholar]
  27. Sasser M. ( 1990). Identification of bacteria by gas chromatography of cellular fatty acids MIDI Technical Note 101 Newark, DE: MIDI Inc.;.
    [Google Scholar]
  28. Skerman V.B.D. ( 1967). A Guide to the Identification of the Genera of Bacteria , 2nd edn.., Baltimore, MD: Williams & Wilkins;.
    [Google Scholar]
  29. Sun H., Wang H.T., Kwon W.S., Kim Y.J., In J.G., Yang D.C. ( 2011;). A simple and rapid technique for the authentication of the ginseng cultivar, Yunpoong, using an SNP marker in a large sample of ginseng leaves. Gene 487 7579 [View Article] [PubMed].
    [Google Scholar]
  30. Takeuchi M., Hatano K. ( 1998;). Union of the genera Microbacterium Orla-Jensen and Aureobacterium Collins et al. in a redefined genus Microbacterium . Int J Syst Bacteriol 48 739747 [View Article] [PubMed].
    [Google Scholar]
  31. Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S. ( 2011;). mega5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28 27312739 [View Article] [PubMed].
    [Google Scholar]
  32. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., Higgins D.G. ( 1997;). The clustal_x windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25 48764882 [View Article] [PubMed].
    [Google Scholar]
  33. Vaz-Moreira I., Lopes A.R., Faria C., Spröer C., Schumann P., Nunes O.C., Manaia C.M. ( 2009;). Microbacterium invictum sp. nov., isolated from homemade compost. Int J Syst Evol Microbiol 59 20362041 [View Article] [PubMed].
    [Google Scholar]
  34. Wayne L.G., Brenner D.J., Colwell R.R., Grimont P.A.D., Kandler O., Krichevsky M.I., Moore L.H., Moore W.E.C., Murray R.G.E., other authors. ( 1987;). International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37 463464 [View Article].
    [Google Scholar]
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